public void UpdateTransporterFromTemplate(ITransporterExpressionContainer transporterContainer, string species, MembraneLocation membraneLocation, TransportType transportType)
{
//we need to retrieve the process name for the given MembraneTupe/Process Type combo
var templateToUse = _transporterContainerTemplateRepository.TransportersFor(species, transporterContainer.Name)
.Where(x => x.MembraneLocation == membraneLocation)
.FirstOrDefault(x => x.TransportType == transportType);
//That should never happen, otherwise we would have a transporter container with an unknown process
if (templateToUse == null)
{
throw new PKSimException(PKSimConstants.Error.CouldNotFindTransporterFor(transporterContainer.Name, membraneLocation.ToString(), transportType.ToString()));
}
transporterContainer.UpdatePropertiesFrom(templateToUse);
}
public override void GlobalContext()
{
base.GlobalContext();
_transporterContainerTemplateRepository = IoC.Resolve <ITransporterContainerTemplateRepository>();
var allTransporters = _transporterContainerTemplateRepository.TransportersFor(_individual.Species.Name, CoreConstants.Organ.Brain);
var influxBBB = allTransporters.Where(x => x.MembraneLocation == MembraneLocation.BloodBrainBarrier)
.FirstOrDefault(x => x.TransportType == TransportType.Influx);
_transporter = _transporterFactory.CreateFor(_individual).DowncastTo <IndividualTransporter>().WithName("TRANS");
var transportContainer = _transporter.ExpressionContainer(CoreConstants.Organ.Brain).DowncastTo <TransporterExpressionContainer>();
transportContainer.UpdatePropertiesFrom(influxBBB);
_individual.AddMolecule(_transporter);
_transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM)
.DowncastTo <PartialProcess>());
_transportProcess.Name = "My Transport Process";
_compound.AddProcess(_transportProcess);
_simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol)
.DowncastTo <IndividualSimulation>();
_simulation.CompoundPropertiesList.First()
.Processes
.TransportAndExcretionSelection
.AddPartialProcessSelection(new EnzymaticProcessSelection {
CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name
});
DomainFactoryForSpecs.AddModelToSimulation(_simulation);
}
public IEnumerable <MembraneLocation> AllProteinMembraneLocationsFor(TransporterExpressionContainerDTO transporterExpressionContainerDTO)
{
return(_transporterContainerTemplateRepository
.TransportersFor(SimulationSubject.Species.Name, transporterExpressionContainerDTO.ContainerName)
.Where(x => x.TransportType == _transporter.TransportType)
.Select(x => x.MembraneLocation)
.Distinct());
}
private void addLiverZoneExpression(Individual individual, IndividualTransporter transporter, string zoneName)
{
var liver = individual.Organism.Organ(CoreConstants.Organ.Liver);
var zone = liver.Compartment(zoneName);
var transportToBile = _transporterContainerTemplateRepository.TransportersFor(individual.Species.Name, zone.Name)
.Where(x => x.MembraneLocation == MembraneLocation.Apical)
.First(x => x.TransportType == TransportType.Efflux);
var transporterContainer = addTransporterExpressionForContainer(individual, transporter, zone, CoreConstants.Groups.ORGANS_AND_TISSUES, transportToBile);
transporterContainer.ClearProcessNames();
transporterContainer.AddProcessName(CoreConstants.Process.BILIARY_CLEARANCE_TO_GALL_BLADDER);
transporterContainer.AddProcessName(CoreConstants.Process.BILIARY_CLEARANCE_TO_DUODENUM);
transporterContainer.RelativeExpression = 100;
transporterContainer.RelativeExpressionNorm = 1;
}
public void SetDefaultSettingsForTransporter(ISimulationSubject simulationSubject, IndividualTransporter transporter, string transporterName)
{
var speciesName = simulationSubject.Species.Name;
transporter.TransportType = _transporterContainerTemplateRepository.TransportTypeFor(speciesName, transporterName);
foreach (var transporterContainer in simulationSubject.AllMoleculeContainersFor <TransporterExpressionContainer>(transporter))
{
//there is a db template
var transporterTemplate = _transporterContainerTemplateRepository
.TransportersFor(speciesName, transporterContainer.LogicalContainerName, transporterName)
.FirstOrDefault();
updateTransporterContainerFromTemplate(transporterContainer, transporterTemplate, transporter.TransportType);
}
if (_transporterContainerTemplateRepository.HasTransporterTemplateFor(speciesName, transporterName))
{
return;
}
//No template was found for the given name. Raise event warning
_eventPublisher.PublishEvent(new NoTransporterTemplateAvailableEvent(transporter));
}
protected override void Context()
{
_repository = A.Fake <ITransporterContainerTemplateRepository>();
_eventPublisher = A.Fake <IEventPublisher>();
_transportDirectionRepository = A.Fake <ITransportDirectionRepository>();
sut = new TransportContainerUpdater(_repository, _eventPublisher);
_fractionExpressedApical = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
_fractionExpressedApicalMucosa = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
_fractionExpressedApicalBone = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL);
//Indicates that this parameter should not be visible to the user and therefore remains unchanged
_fractionExpressedApicalBone.Visible = false;
_individual = A.Fake <ISimulationSubject>();
_individual.Species.Name = _species;
_transporter = new IndividualTransporter {
TransportType = TransportType.Efflux, Name = "toto"
};
var organism = new Organism();
var mucosa = new Container().WithName(CoreConstants.Compartment.MUCOSA).WithParentContainer(organism);
var liver = new Container().WithName(CoreConstants.Organ.LIVER).WithParentContainer(organism);
var liverCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver);
var kidney = new Container().WithName(CoreConstants.Organ.KIDNEY).WithParentContainer(organism);
var kidneyCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(kidney);
var bone = new Container().WithName(CoreConstants.Organ.BONE).WithParentContainer(organism);
var boneInterstitial = new Container().WithName(CoreConstants.Compartment.INTERSTITIAL).WithParentContainer(bone);
_transporterWithTemplate = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(liverCell);
_transporterWithoutTemplate = new TransporterExpressionContainer
{
TransportDirection = TransportDirectionId.EffluxIntracellularToInterstitial
}
.WithParentContainer(kidneyCell);
_transporterInMucosa = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(mucosa);
_transporterInBone = new TransporterExpressionContainer {
TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular
}
.WithParentContainer(boneInterstitial);
_transporterInMucosa.Add(_fractionExpressedApicalMucosa);
_transporterWithoutTemplate.Add(_fractionExpressedApical);
_transporterInBone.Add(_fractionExpressedApicalBone);
A.CallTo(() => _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(_transporter))
.Returns(new[] { _transporterWithTemplate, _transporterWithoutTemplate, _transporterInMucosa, _transporterInBone });
_transporterContainerTemplate = new TransporterContainerTemplate {
TransportType = TransportType.Influx
};
_allTransporterTemplates.Add(_transporterContainerTemplate);
A.CallTo(() => _repository.HasTransporterTemplateFor(_species, _transporter.Name)).Returns(true);
A.CallTo(() => _repository.TransportTypeFor(_species, _transporter.Name)).Returns(TransportType.Influx);
A.CallTo(() => _repository.TransportersFor(_species, liver.Name, _transporter.Name)).Returns(_allTransporterTemplates);
A.CallTo(() => _repository.TransportersFor(_species, kidney.Name, _transporter.Name)).Returns(new List <TransporterContainerTemplate>());
}
